Research workbench
Crystal structure of the human retinoid X receptor DNA-binding domain bound to the human mep DR1 response element, pH 7.0
Analyse Crystal structure of the human retinoid X receptor DNA-binding domain bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FBQ
- Type
- protein + DNA
- Length
- 195 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; DNA (5'- D(*CP*TP*GP*GP*GP*TP*CP*AP*AP*AP*GP*TP*TP*CP*AP…
- UniProt
- P19793
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 80 | 33% helix, 13% strand | P19793 |
| B | Retinoic acid receptor rxr-alpha | protein | 81 | 35% helix, 10% strand | P19793 |
| C | DNA (5'- D(*CP*TP*GP*GP*GP*TP*CP*AP*AP*AP*GP*TP*TP*CP*AP*TP*C)-3') | dna | 17 | — | — |
| D | DNA (5'- D(*GP*AP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*CP*CP*CP*AP*G)-3') | dna | 17 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.57 | 0.78 | 37 | empty |
| 2 | 177 | 0.45 | 0.75 | 21 | empty |
| 3 | 93 | 0.40 | 0.78 | 18 | empty |
| 4 | 85 | 0.35 | 0.75 | 15 | empty |
| 5 | 62 | 0.26 | 0.73 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 774 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- A–C · 481 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 479 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–D · 467 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 414 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 6FBQ · Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P19793
- Elsewhere: RCSB PDB 6FBQ · PDBe 6FBQ · UniProt P19793
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